Code to calculate the Jacobian-weighted energy, entropy, and free-energy profiles along a nonlinear latent space coordinate.
Right now, the code is designed to work on a two-dimensional input space with a latent space that is either one- or two-dimensional, but the code can be generalized for an input and latent space of arbitrary dimensionality.
Index of Codes:
util.py: Python file containing a set of utility functions required to run the Jacobian scripts
jacobian.py: Python file containing the definitions of functions that calculate the Jacobian-corrected free-energy, energy (or enthalpy), and entropy along each latent space coordinate. Optionally ouputs plots of the free-energy profiles and projections of the latent variables and their cooresponding gradients along the input two-dimensional coordinate space.
run_jacobian.ipynb: Jupyter notebook showing how to run the Jacobian codes for a pair of analytical potentials, one of which has a one-dimensoonal latent space and the other which has a two-dimensional latent space.